Tip Dating in BEAST

Understanding how robust the molecular clock is a critical step for many evolutionary analyses. Usually when I get given a set of aligned sequences I turn to TempEst to test the ‘clocklikeness’ of the data. However, after the release of ‘TIPDATINGBEAST’ (I’ll call it TDBEAST fr short) I may turn to TempEst much less often. Whist TempEst is useful in getting some qualitative idea of the temporal signal in the data but I find it annoying that its hard to drill down to find what sequences sequences that are leading to bias.¬† Furthermore, TempEst¬† is sensitive to the input tree which can lead to problems and I have had issues with guessDates as well which is slightly irritating. TDBEAST solves lots of these issues and more and provides a robust method to test how ‘clock-like’ your sequences are. The TDBEAST R package does 2 things using BEAST log files and .xml files:

1. Uses a date randomization test to measure temporal signal and provides a nice visualization  to check results.

2. Uses a leave one out cross validation to work out the likely culprits that could be skewing results. These sequences, for example, could have the wrong date assigned to them by mistake – this is a real problem when working on sequences from the field.

Whilst I’m having a few teething issues with the code, overall the ‘how to’ guide is excellent and the code seems straight forward. TDBEAST definitely seems like a valuable addition to my phylogenetic tool box.

Here are the links: http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12603/full

http://onlinelibrary.wiley.com/store/10.1111/1755-0998.12603/asset/supinfo/men12603-sup-0001-SupInfo.pdf?v=1&s=3c884538553c0742a65d37dfe6fdeceaf2326573

https://cran.r-project.org/web/packages/TipDatingBeast/TipDatingBeast.pdf

 

 

 

 

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